org.biojava.nbio.structure.symmetry.core

Class QuatSymmetryResults

java.lang.Object

org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

public class QuatSymmetryResults
extends Object

Holds the results of quaternary symmetry perception obtained with QuatSymmetryDetector.

Author:

Peter Rose, Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
QuatSymmetryResults(List<SubunitCluster> clusters, HelixLayers helixLayers, SymmetryPerceptionMethod method) Constructor for roto-translational symmetries.
QuatSymmetryResults(List<SubunitCluster> clusters, RotationGroup rotationGroup, SymmetryPerceptionMethod method) Constructor for rotational symmetries.

Method Summary

Modifier and Type	Method and Description
HelixLayers	getHelixLayers()
SymmetryPerceptionMethod	getMethod()
RotationGroup	getRotationGroup()
QuatSymmetryScores	getScores()
String	getStoichiometry()
Structure	getStructure()
List<SubunitCluster>	getSubunitClusters() Returns the List of SubunitCluster used to calculate symmetry.
int	getSubunitCount() Return the number of Subunits involved in the symmetry.
List<Subunit>	getSubunits() Returns the List of Subunits used to calculate symmetry.
String	getSymmetry()
boolean	isLocal() A local result means that only a subset of the original Subunits was used for symmetry determination.
boolean	isPseudoStoichiometric()
boolean	isPseudosymmetric() A symmetry result is pseudosymmetric when using pseudostoichiometry extended the symmetry over the
void	setPseudosymmetric(boolean pseudosymmetric) A symmetry result is pseudosymmetric when using pseudostoichiometry extended the symmetry over the
void	setStructure(Structure structure)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

QuatSymmetryResults

public QuatSymmetryResults(List<SubunitCluster> clusters,
                           RotationGroup rotationGroup,
                           SymmetryPerceptionMethod method)

Constructor for rotational symmetries.

Parameters:

clusters - List of SubunitCluster used to calculate symmetry

rotationGroup -

method -

QuatSymmetryResults

public QuatSymmetryResults(List<SubunitCluster> clusters,
                           HelixLayers helixLayers,
                           SymmetryPerceptionMethod method)

Constructor for roto-translational symmetries.

Parameters:

clusters - List of SubunitCluster used to calculate symmetry

helixLayers -

method -

Method Detail

getSubunitClusters

public List<SubunitCluster> getSubunitClusters()

Returns the List of SubunitCluster used to calculate symmetry.

Returns:

an unmodifiable view of the original List

getSubunits

public List<Subunit> getSubunits()

Returns the List of Subunits used to calculate symmetry.

Returns:

an unmodifiable view of the List

getSubunitCount

public int getSubunitCount()

Return the number of Subunits involved in the symmetry.

Returns:

the number of Subunits

getRotationGroup

public RotationGroup getRotationGroup()

Returns:

rotation group (point group) information representing rotational quaternary symmetry.

getHelixLayers

public HelixLayers getHelixLayers()

Returns:

helix layers (layer lines) as a list of helices that describe a helical structure.

getMethod

public SymmetryPerceptionMethod getMethod()

Returns:

the method used for symmetry perception.

getSymmetry

public String getSymmetry()

Returns:

the symmetry group symbol. For point groups returns the point group symbol and for helical symmetry returns "H".

getScores

public QuatSymmetryScores getScores()

Returns:

the quaternary scores as an object

getStoichiometry

public String getStoichiometry()

isPseudoStoichiometric

public boolean isPseudoStoichiometric()

isLocal

public boolean isLocal()

A local result means that only a subset of the original Subunits was used for symmetry determination.

Returns:

true if local result, false otherwise

isPseudosymmetric

public boolean isPseudosymmetric()

A symmetry result is pseudosymmetric when using pseudostoichiometry extended the symmetry over the

Returns:

true is pseudosymmetric, false otherwise

setPseudosymmetric

public void setPseudosymmetric(boolean pseudosymmetric)

A symmetry result is pseudosymmetric when using pseudostoichiometry extended the symmetry over the

Parameters:

pseudosymmetric - true if pseudosymmetric, false otherwise

getStructure

public Structure getStructure()

setStructure

public void setStructure(Structure structure)

toString

public String toString()

Overrides:

toString in class Object